CUSTOM GENE ARRAY CONSTRUCTION
Gene sequences spotted onto a solid support matrix are called gene arrays (also referred to as microarrays, macroarrays, gene chips, or DNA arrays). An array can consist of hundreds to thousands of cDNAs or oligonucleotide gene sequences spotted in an organized pattern. The arrays can be probed with mRNA obtained from treated tissues or cells in order to obtain a semi-quantitative measure of expression for each of the genes present on the array. Thus, gene arrays can be used to simultaneously measure the expression level of all the genes that are affixed to the surface. Because thousands of genes can be queried at one time, this global analysis of gene expression can be quite useful in measuring the effects of toxicological exposure, as well as other areas of research.
Are you interested in microarray technology, but...
- Species of interest not yet sequenced? EcoArray provides library construction (suppression subtractive hybridization libraries and normalized libraries) as a first step in gene discovery. We can help you with sequencing and array design.
- No commercially available microarray for your model organism? EcoArray can assemble your sequences (proprietary and/or public ESTs), BLAST to public databases, design the probes, and manage your array design.
For large (>800 genes) microarray construction, we recommend the Agilent platform.
EcoArray selected Agilent Technologies as the manufacturer of our microarrays for environmental toxicology. Agilent Technologies is a leading supplier of genomics and proteomics products. Using their SurePrint inkjet deposition of in situ synthesized 60-mer oligonucleotides, all microarrays are manufactured on superior quality 1” x 3” (24.2 mm x 76.2 mm) treated glass slides for overall excellent performance. This process minimizes variability across each production lot (batch to batch) and provides the highest consistency in slide-to-slide comparisons. These glass slide microarrays are designed for either a one- or two-color (cyanine-3 and cyanine-5) labeling reaction, the most reliable and sensitive methods for detecting differentially expressed genes. Agilent’s Feature Extraction software, when used with a high-resolution (5mm) scanner, provides QA metrics for each individual microarray, ensuring quality results.
For small (<800 gene) microarraconstruction please contact us
EcoArray's expert technical staff can print cDNA on a nylon membrane array containing up to 768 genes (spotted singly; otherwise 384 genes spotted in duplicate) in your particular species of interest. These genes belong to you, and you alone, and EcoArray will work with you on obtaining the genes. It is possible for us to do the gene discovery by means of a library or subtractive hybridization (see Services), or you may send us the cDNA to be spotted. Each spot on a custom-printed cDNA array contains 10 nanograms of PCR product (cDNA). These are high quality arrays with low background that give highly reproducible results.
Arrays are sold in batches of twenty. In addition, you receive:
- A complete list of genes that were spotted on the membrane and their locations.
- Free access to BlastQuest, a searchable website database that contains pertinent information obtained for each gene spotted such as expectation (e) values, bit scores, accession numbers, and links to sequence information at PubMed, NCBI.
- Twenty aliquots of spiking RNA (one per membrane).
- Complete hybridization protocol. Recommended hybridization: The arrays have been optimized using a a-33P label probe with minimal RNA as the starting material (2μgs of total RNA) that is labeled with a a-33P label. The membranes can also be labeled with 32P or a chemiluminescent label following manufacturers recommendations. (EcoArray can perform hybridization of nylon membrane arrays in our lab as a service. See our services page.)
This image is an example of EcoArray's custom cDNA arry printed for the Atlantic bottlenose dolphin (Tursiops truncatus). Genes were discovered by making libraries of RNA obtained from blood samples. This array has 480 features representing 475 genes plus positive and negative controls.